Commits · 823f5bc0496c940fc39c70493cd596ca9c139fea · Mutalyzer / mutalyzer2

29 Nov, 2012 1 commit

Vermaat authored Nov 29, 2012

Changed codes:

    WCDSSELECTED    -> WCDS
    WCDS            -> WCDS_OTHER
    WSPLICESELECTED -> WSPLICE
    WSPLICE         -> WSPLICE_OTHER


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@644 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

823f5bc0

28 Nov, 2012 2 commits

Fixed the command line interface, it is not very pretty yet, but it now is · be574870

Laros authored Nov 28, 2012

fully functional again.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@643 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

be574870

Frameshift detection error (#124) fixed. · 4e9bd5f2

Laros authored Nov 28, 2012


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@642 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e9bd5f2

26 Nov, 2012 1 commit

Have separate WCDS and WCDSSELECTED codes (#98) · 137474bd

Vermaat authored Nov 26, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@641 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

137474bd

22 Nov, 2012 1 commit

Create databases in install script (fixes #112) · 6a38f261

Vermaat authored Nov 22, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@640 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6a38f261

15 Nov, 2012 1 commit

Some unit tests for mtDNA position converter · 455ae1e2

Vermaat authored Nov 15, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@639 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

455ae1e2

14 Nov, 2012 4 commits

Support organelle types in position converter · 095bea67

Vermaat authored Nov 14, 2012

Keep organelle type ('chromosome' or 'mitochondrion') in chromosome database
table and use it to choose between g. and m. positioning.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@638 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

095bea67

Use temporary directory in remote deployment · 75340eb2

Vermaat authored Nov 14, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@637 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

75340eb2

Fix for incorrect SQL in r635 · efaaed66

Vermaat authored Nov 14, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@636 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

efaaed66

Genomic reference transcript mappings · f17e991f

Vermaat authored Nov 14, 2012

Support genomic references in the mapping database. At the moment, this is
only tested with mtDNA genes, but should in clear the way for NG_ mappings
as well.
Mappings for mtDNA genes can be added to the database using the command line
tool mutalyzer-mapping-import.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@635 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f17e991f

08 Nov, 2012 4 commits

Open development for 2.0.beta-24 · 5cfd21d8

Vermaat authored Nov 08, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@634 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5cfd21d8

Release 2.0.beta-23 · 905284e9

Vermaat authored Nov 08, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@632 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

905284e9

Add new script to setup.py · 86f7e0ed

Vermaat authored Nov 08, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@631 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

86f7e0ed

Script to load mapping info from UCSC · 9d0ceda1

Vermaat authored Nov 08, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@630 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9d0ceda1

05 Nov, 2012 1 commit

Have latest refseq mapping in cron example · 03391977

Vermaat authored Nov 05, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@629 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

03391977

02 Nov, 2012 2 commits

Open development for 2.0.beta-23 · 36bde44c

Vermaat authored Nov 02, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@628 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

36bde44c

Release 2.0.beta-22 · b9498dd9

Vermaat authored Nov 02, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@626 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b9498dd9

29 Oct, 2012 2 commits

Catch IncompleteRead error in dbSNP communication · 1f22cc21

Vermaat authored Oct 29, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@625 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1f22cc21

Write monitor errors to stderr · f2448ac8

Vermaat authored Oct 29, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@624 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f2448ac8

26 Oct, 2012 1 commit

Mutalyzer instance monitor script · 8c21b407

Vermaat authored Oct 26, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@623 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8c21b407

20 Oct, 2012 1 commit

Added a first draft of the Mutalyzer 2.0 paper. · 6e5795bc

Laros authored Oct 20, 2012



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@622 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6e5795bc

05 Oct, 2012 4 commits

Webservice interface for submitting batch jobs · a7248a86

Vermaat authored Oct 05, 2012


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@621 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a7248a86

Fix unit test for restriction site analysis · 8f31e51d

Vermaat authored Oct 05, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@620 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8f31e51d

Use functools.wraps in decorators · 3a7c3a61

Vermaat authored Oct 05, 2012

This makes sure docstring and name are inherited from the decorated
definition. Fixes decorated unit tests, which previously where skipped
since their name did not start with test_ after decorating.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@619 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3a7c3a61

Typo · be4bdc68

Vermaat authored Oct 05, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@618 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

be4bdc68

04 Oct, 2012 6 commits

Warn on missing positioning scheme (fixes #114) · 1ec48b68

Vermaat authored Oct 04, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@617 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1ec48b68

Do not crash on EST reference · b3ca7327

Vermaat authored Oct 04, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@616 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b3ca7327

Revert skip_depth=2 in JSON output · 7cac3ed8

Vermaat authored Oct 04, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@615 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7cac3ed8

Get Spyne from LUMC GitHub repository · 52ed8aac

Vermaat authored Oct 04, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@614 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

52ed8aac

Use skip_depth=2 for JSON output (again) · dce1e05e

Vermaat authored Oct 04, 2012

See https://github.com/arskom/spyne/issues/159


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@613 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

dce1e05e

Remove Spyne monkey patch, implemented upstream · de232952

Vermaat authored Oct 04, 2012

See https://github.com/arskom/spyne/issues/158


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@612 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

de232952

01 Oct, 2012 1 commit

Optional Piwik analytics integration · 590fc39e

Vermaat authored Oct 01, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@611 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

590fc39e

28 Sep, 2012 1 commit
- Fixed some errors and unclear things in the presentation of 16-09-12. · 0879ed97
  Laros authored Sep 28, 2012
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@610 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
  0879ed97
26 Sep, 2012 1 commit

Fixed a typo in the latest presentation. · 91a20e3c

Laros authored Sep 26, 2012


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@609 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

91a20e3c

25 Sep, 2012 1 commit

Added a presentation that covers the description extractor. · 77325486

Laros authored Sep 25, 2012



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@608 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

77325486

24 Sep, 2012 3 commits

Maximum matrix size for description extractor · 3185a420

Vermaat authored Sep 24, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@607 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3185a420

Fix batch form javascript · 90530865

Vermaat authored Sep 24, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@606 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

90530865

Case insensitive gene reference loader (#118) · 58bdbf60

Vermaat authored Sep 24, 2012

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@605 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

58bdbf60

22 Aug, 2012 2 commits
- Fix regression r599: initial visibility in reference file loader form · 4170f706
  Vermaat authored Aug 22, 2012
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@604 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
  4170f706
- Fix regression r599: clear fields instead of reset · f7f90e57
  Vermaat authored Aug 22, 2012
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@603 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
  f7f90e57